Dependencies

UNIX

• bash
• make
• g++ of 2017 standard
• sed, awk, bc, sort, date, gzip, cut, grep, dirname, unix2dos

To compute dissimilarities between biological objects

• Prodigal ver. 2.6.3 - for prokaryotic genomes
• GeneMark-ES ver. 4.39 - for eukaryotic genomes
• HMMER ver. 3.1b2 - for genomes
• BUSCO ver. 10 - HMM library for genomes
• NCBI BLAST ver. 2.6.0+ - for sequences
• Pfam - HMM library for genomes

To build an incremental tree

• UGE ver. 8.6.7 - Univa Grid Engine for parallelization
• SQL Server ver. 17.9.1
  • Database on a server
  • sqsh-ms on a client

To compute taxonomy miscongruence

• SQL Server ver. 17.9.1